PXD025223

PXD025223 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Comparative proteomic and metabolomic analysis of human osteoblasts differentiated from dental pulp stem cells
Description	The current global situation points to the trend of the aging population. Along with the growth of population diseases, the pressure to develop new cell-based or drug-based therapies is increasing. One from main challenges in the field of regenerative medicine is large bones healing and osteoporosis, mainly postmenopausal women, treatment. To understand molecular processes which underlying bone development and turnover, osteogenic differentiation using specific media was applied. Differentiation process imitating real osteogenesis is associated with proteome and metabolome changes resulting in various signaling pathways activation. Proteome was profiled by ultrahigh-performance liquid chromatography and comprehensively quantified by ion mobility enhanced mass spectrometry. From 2267 reproducibly quantified proteins, 432 were differentially abundant by strict statistic and effect size criteria. Metabolome profiling was carried out nuclear magnetic resonance in resulting 27 reproducibly quantified metabolites. From them, 8 were statistically significant and differentially abundant. KEGG and MetaboAnalyst analysis indicated several metabolic pathways involved in osteogenic process. Enrichment analysis of differentialy abundant proteins reported PPAR, FoxO, IL-7 signaling pathways, thyroid hormones and steroid biosynthesis, mineral absorption, JAK-STAT and fatty acid degradation pathways as cascades with prominent impact to osteoinduction. Among them, enrichment analysis of significant metabolites showed Aminoacyl-tRNA biosynthesis as well as Valine, leucine, isoleucine metabolism together with phenylalanine, tyrosine and tryptophane metabolism as pathways which promotes osteodifferentiation. Moreover, we also selected few identified pathways which do not reported enrichment score, but have been described in the literature as majority. These cascades underline the complexity of the whole potential osteogenic mechanism. We also proposed promising targets for next validation in patient samples, what is step forward to influence of bone and/or oral defects.
HostingRepository	PRIDE
AnnounceDate	2021-11-03
AnnouncementXML	Submission_2021-11-03_03:21:17.384.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD025223
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Maksym Danchenko
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	SYNAPT G2-Si

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2021-04-06 07:15:51	ID requested
⏵ 1	2021-11-03 03:21:18	announced

Publication List

Nov, á, kov, á S, Danchenko M, Okaj, č, ekov, á T, Baranovi, č, ov, á E, Kov, á, č A, Grend, á, r M, Beke G, P, á, le, š, ov, á J, Strn, á, del J, Jan, í, č, kov, á M, Hala, š, ov, á E, Š, kovierov, á H, Comparative Proteomic and Metabolomic Analysis of Human Osteoblasts, Differentiated from Dental Pulp Stem Cells, Hinted Crucial Signaling Pathways Promoting Osteogenesis. Int J Mol Sci, 22(15):(2021) [pubmed]

Nov, á, kov, á S, Danchenko M, Okaj, č, ekov, á T, Baranovi, č, ov, á E, Kov, á, č A, Grend, á, r M, Beke G, P, á, le, š, ov, á J, Strn, á, del J, Jan, í, č, kov, á M, Hala, š, ov, á E, Š, kovierov, á H, Comparative Proteomic and Metabolomic Analysis of Human Osteoblasts, Differentiated from Dental Pulp Stem Cells, Hinted Crucial Signaling Pathways Promoting Osteogenesis. Int J Mol Sci, 22(15):(2021) [pubmed]

Keyword List

submitter keyword: osteodifferentiation, label-free quantification, NMR, signaling pathways, bone metabolism, mineralization phase, late osteoblast, Homo sapiens

submitter keyword: osteodifferentiation, label-free quantification, NMR, signaling pathways, bone metabolism, mineralization phase, late osteoblast, Homo sapiens

Contact List

Andrej Kováč
contact affiliation	Institute of Neuroimmunology of Slovak Academy of Sciences
contact email	andrej.kovac@savba.sk
lab head
Maksym Danchenko
contact affiliation	Plant Science and Biodiversity Center SAS
contact email	maxymdan@gmail.com
dataset submitter

Full Dataset Link List

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PRIDE project URI

Dataset FTP location
NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/09/PXD025223

PRIDE project URI

Repository Record List

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